{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:26:17Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.5, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09526-3959-7ea1-a370-ff0da71cc212\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: Immunoglobulin-like domain superfamily\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 th", "usd": 0.0, "recall": true }, "codex": { "seconds": 72.3, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09526-3952-7b80-9be1-3e187e7dd5c0\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Immunoglobulin-like domain superfamily\nRegistry id: vr.tr.immunoglobulin-like-domain-superfamily\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:52:10+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "revisions": [ { "at": "2026-10-07T11:32:49+00:00", "engine": "codex", "fields": [ "definition", "distinguishing_features", "in_scope", "out_of_scope", "purpose", "scope_statement", "visual_identification" ], "answering_review": "70912342e960f394a9bc326558e9f9dbd2ea0270440a5ba064631a15f5350012" }, { "at": "2026-10-08T18:49:12+00:00", "engine": "codex", "fields": [ "agent_conduct" ], "answering_review": "1a849f3c38294d3ea42755352b1f81fa7e3894b8853437ee61771a98055b8050" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-08T18:54:39+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q41797304", "registryId": "vr.tr.immunoglobulin-like-domain-superfamily", "name": "Immunoglobulin-like domain superfamily", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q41797304/", "model": { "registry_id": "vr.tr.immunoglobulin-like-domain-superfamily", "name": "Immunoglobulin-like domain superfamily", "purpose": "Enable an agent to assess protein membership in the immunoglobulin superfamily, describe supporting domain architecture and constrain functional inferences to available evidence.", "definition": "The immunoglobulin superfamily is a large superfamily of cell-surface and soluble proteins containing one or more immunoglobulin-like domains, with members involved in immune functions, cell recognition, adhesion and other biological roles.", "scope_statement": "This model owns the protein-level superfamily of cell-surface and soluble proteins characterised by immunoglobulin-like domains, its membership criteria and biological diversity; domain-level classifications provide supporting evidence rather than defining a separate referent.", "in_scope": [ "Superfamily identity concerns proteins rather than isolated domain occurrences.", "Membership assessment uses evidence about protein identity and immunoglobulin-like domain architecture.", "Domain structure, subtype and repetition support descriptions of member proteins.", "Members include cell-surface and soluble proteins with diverse biological roles.", "Functional interpretation distinguishes protein-specific evidence from shared structural features." ], "out_of_scope": [ "Standalone classification of immunoglobulin-like domains as the primary referent is outside scope.", "Complete models of antibody isotypes and immune repertoires are outside scope.", "Gene regulation, organism physiology and immune-system models are outside scope.", "Purified protein products, formulation, purity and manufacturing are outside scope.", "Proteins lacking evidence of membership are outside scope even if they contain a superficially similar beta-sandwich structure." ], "distinguishing_features": [ "Membership is assigned to a protein, with its immunoglobulin-like domains providing supporting evidence.", "Member proteins contain one or more immunoglobulin-like domains, typically formed from opposing antiparallel beta sheets.", "A domain database assignment must be distinguished from a curated protein-superfamily assignment.", "An immune-system role is neither sufficient nor required to establish membership.", "Shared domain architecture does not establish identical biological functions across member proteins." ], "characteristics": [ { "name": "Classification anchor", "kind": "relation", "unit_or_values": "Database accession, entry type, release, and exact/broader/narrower/overlapping mapping", "why_it_matters": "Prevents similarly named fold, domain, and superfamily records from becoming interchangeable." }, { "name": "Domain interval", "kind": "measurement", "unit_or_values": "Start and end residue positions, numbering convention, host accession, and sequence version", "why_it_matters": "Identifies the actual molecular region being classified." }, { "name": "Assignment status", "kind": "state", "unit_or_values": "Supported, provisional, conflicting, rejected, or unassessed", "why_it_matters": "Controls whether an agent can accept membership or must seek additional evidence." }, { "name": "Sequence-match support", "kind": "measurement", "unit_or_values": "Method-specific score, E-value where applicable, coverage percentage, and signature release", "why_it_matters": "Makes computational assignments assessable without imposing a universal threshold." }, { "name": "Strand topology", "kind": "category", "unit_or_values": "Observed strand labels, sheet membership, connectivity, and unresolved segments", "why_it_matters": "Distinguishes compatible domain architecture from superficial shape similarity." }, { "name": "Domain subtype", "kind": "category", "unit_or_values": "V-set, C1-set, C2-set, I-set, another source-defined subtype, or unresolved", "why_it_matters": "Records finer classification without forcing every member into a predefined subtype." }, { "name": "Core and disulfide integrity", "kind": "state", "unit_or_values": "Observed, predicted, disrupted, absent, or unresolved, with residue-level evidence", "why_it_matters": "Separates lineage membership from the folding state of a particular domain occurrence." }, { "name": "Host-protein architecture", "kind": "relation", "unit_or_values": "Host protein, domain ordinal, neighboring domains, linker intervals, and localization evidence", "why_it_matters": "Provides context for interactions and distinguishes repeated domain copies." }, { "name": "Domain-attributed binding", "kind": "measurement", "unit_or_values": "Partner identity; Kd in mol/L where measured; assay, construct, and conditions", "why_it_matters": "Allows functional claims to be tied to a tested domain rather than transferred from a whole protein." } ], "affordances": [ "Evaluate candidate sequence intervals against a versioned superfamily classification.", "Compare observed or predicted strand topology with supported domain representatives.", "Map repeated domain occurrences and their boundaries within a host protein.", "Identify domain assignments needing structural inspection or experimental validation.", "Assess whether interaction or variant evidence supports a domain-specific claim.", "Revise membership and subtype annotations when classification evidence changes." ], "agent_conduct": { "may": [ "Describe the immunoglobulin protein superfamily and its members from structural biology sources.", "Assess protein-superfamily membership using recognized databases and domain annotations with stated confidence." ], "must_not": [ "Present a domain prediction as confirmed structure without evidence.", "Claim that a member protein is a drug target or disease cause beyond the evidence.", "Help design proteins or antibodies for harming people." ], "requires_human": [ "Publishing structure or function claims that inform clinical decisions." ] }, "ethics": { "considerations": [ "Errors in protein annotation spread through databases and research.", "Antibody and receptor research has dual-use and clinical stakes." ], "affected_parties": [ "Researchers and database users", "Patients in clinical research" ] }, "owners": { "steward": "Nobody owns the concept; curated protein databases maintain its classification.", "master_systems": [ "Protein family and structure databases" ] }, "visual_identification": [ "Molecular structure representations may show immunoglobulin-like beta-sandwich domains within a member protein, but appearance alone does not establish protein-superfamily membership." ], "failure_modes_and_hazards": [ "Over-broad annotation can mislabel unrelated proteins." ], "what_it_is_for": [ "The immunoglobulin-like domain superfamily is encountered in protein structure analysis, sequence annotation and studies of immune recognition and cell adhesion.", "Its classification helps compare domains across antibodies, receptors and other proteins, but membership alone does not establish a particular biological function." ], "facets_not_applicable": { "interfaces": "No universally applicable formal standard, law or official classification governs membership in this structural superfamily." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q41797304: Immunoglobulin-like domain superfamily", "url": "https://www.wikidata.org/wiki/Q41797304", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Immunoglobulin superfamily", "url": "https://en.wikipedia.org/wiki/Immunoglobulin_superfamily", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "superfamily-identity-and-boundaries", "name": "Superfamily identity and boundaries", "description": "Establish what the registered superfamily denotes and how neighboring classifications relate to it.", "rationale": "The same vocabulary can refer to a structural fold, a domain classification, or whole proteins.", "layers": [ { "id": "classification-anchor", "name": "Classification anchor", "description": "Resolve the registry name to an authoritative domain-superfamily concept.", "findings": [ { "id": "registry-to-classification-mapping", "name": "Registry-to-classification mapping", "description": "Record the evidence connecting this registry entry to an external classification without assuming name equality proves equivalence.", "questions": [ { "text": "Does the registry's originating record explicitly identify InterPro IPR036179 or another classification?", "kind": "provenance", "id": "registry-to-classification-mapping-q01" }, { "text": "What membership definition and release establish the intended superfamily?", "kind": "definition", "id": "registry-to-classification-mapping-q02" } ] } ] }, { "id": "neighboring-domain-concepts", "name": "Neighboring domain concepts", "description": "Distinguish domain, fold, subtype, and whole-protein concepts.", "findings": [ { "id": "classification-overlap", "name": "Classification overlap", "description": "Represent broader, narrower, and overlapping classifications explicitly.", "questions": [ { "text": "How does the selected superfamily relate to IPR007110 and IPR013783 in the cited release?", "kind": "boundary", "id": "classification-overlap-q01" }, { "text": "Which uses of 'immunoglobulin superfamily' refer to whole proteins rather than this domain-level concept?", "kind": "boundary", "id": "classification-overlap-q02" } ] } ] } ] }, { "id": "domain-detection-and-delimitation", "name": "Domain detection and delimitation", "description": "Establish which residues form a candidate member and how strongly the evidence supports that assignment.", "rationale": "An apparent match can be partial, overlap another annotation, or conflate neighboring repeats.", "layers": [ { "id": "sequence-intervals", "name": "Sequence intervals", "description": "Locate each domain occurrence on a specific protein sequence.", "findings": [ { "id": "domain-boundary-evidence", "name": "Domain boundary evidence", "description": "Record proposed residue boundaries and distinguish missing sequence from genuine domain variation.", "questions": [ { "text": "Which accession, isoform, sequence version, and residue interval identify this occurrence?", "kind": "provenance", "id": "domain-boundary-evidence-q01" }, { "text": "Do sequence and structure evidence support the same boundaries, particularly between tandem domains?", "kind": "boundary", "id": "domain-boundary-evidence-q02" } ] } ] }, { "id": "membership-support", "name": "Membership support", "description": "Assess computational and structural support for classification.", "findings": [ { "id": "assignment-strength-and-conflicts", "name": "Assignment strength and conflicts", "description": "Keep evidence strength and conflicting assignments visible rather than reducing them to a binary label.", "questions": [ { "text": "Which signatures, database releases, scores, coverage values, and acceptance thresholds support membership?", "kind": "measurement", "id": "assignment-strength-and-conflicts-q01" }, { "text": "What additional evidence is needed when sequence and structural classifications disagree?", "kind": "action", "id": "assignment-strength-and-conflicts-q02" } ] } ] } ] }, { "id": "fold-topology-and-variation", "name": "Fold topology and variation", "description": "Describe the domain's structural core and supported departures from representative architectures.", "rationale": "Topology and local variation provide stronger distinctions than a generic beta-sandwich description.", "layers": [ { "id": "beta-sandwich-core", "name": "Beta-sandwich core", "description": "Assess sheet organization, strand connectivity, and core packing.", "findings": [ { "id": "topological-compatibility", "name": "Topological compatibility", "description": "Record structural observations needed to compare a candidate with classified representatives.", "questions": [ { "text": "Which strands form each sheet, and what connectivity supports an immunoglobulin-like topology?", "kind": "measurement", "id": "topological-compatibility-q01" }, { "text": "Which structural observations distinguish this candidate from other beta-sandwich folds?", "kind": "boundary", "id": "topological-compatibility-q02" } ] } ] }, { "id": "subtype-and-local-variation", "name": "Subtype and local variation", "description": "Describe subtype evidence, loop differences, insertions, and stabilizing features.", "findings": [ { "id": "supported-structural-subtype", "name": "Supported structural subtype", "description": "Treat subtype labels as evidence-based refinements rather than universal requirements.", "questions": [ { "text": "Which strand and sequence features justify a V-set, C1-set, C2-set, I-set, or other source-defined assignment?", "kind": "definition", "id": "supported-structural-subtype-q01" }, { "text": "Which loops, insertions, core residues, and disulfide connections are observed, predicted, or unresolved?", "kind": "measurement", "id": "supported-structural-subtype-q02" } ] } ] } ] }, { "id": "protein-architecture-and-interactions", "name": "Protein architecture and interactions", "description": "Place the domain within its host protein and evaluate domain-specific contributions.", "rationale": "A shared domain architecture does not establish a shared ligand, immune role, or whole-protein function.", "layers": [ { "id": "host-and-repeat-context", "name": "Host and repeat context", "description": "Describe neighboring domains, linkers, and biological placement.", "findings": [ { "id": "domain-context", "name": "Domain context", "description": "Identify the occurrence within a multidomain protein and record context without inheriting unsupported properties.", "questions": [ { "text": "What is this domain's ordinal position, and which domains and linkers flank it?", "kind": "definition", "id": "domain-context-q01" }, { "text": "What evidence establishes its cellular location and whether the studied construct preserves native domain neighbors?", "kind": "provenance", "id": "domain-context-q02" } ] } ] }, { "id": "interaction-attribution", "name": "Interaction attribution", "description": "Separate tested domain interactions from functions inferred from the host protein.", "findings": [ { "id": "domain-specific-functional-evidence", "name": "Domain-specific functional evidence", "description": "Connect interaction claims to tested interfaces, constructs, and conditions.", "questions": [ { "text": "Which experiments attribute binding or a structural role to this domain rather than to the complete protein?", "kind": "provenance", "id": "domain-specific-functional-evidence-q01" }, { "text": "What partner, interface residues, affinity measurements, and assay conditions support the attributed interaction?", "kind": "measurement", "id": "domain-specific-functional-evidence-q02" } ] } ] } ] }, { "id": "structural-state-and-inference-limits", "name": "Structural state and inference limits", "description": "Assess the reliability of a domain representation and determine which downstream uses its evidence supports.", "rationale": "Membership can remain meaningful even when a variant, construct, or predicted structure does not establish an intact functional domain.", "layers": [ { "id": "representation-and-folding-state", "name": "Representation and folding state", "description": "Distinguish native sequence, experimental constructs, predicted structures, and observed folding states.", "findings": [ { "id": "domain-integrity", "name": "Domain integrity", "description": "Track truncations, substitutions, unresolved regions, and evidence of structural disruption.", "questions": [ { "text": "Which sequence changes or missing residues affect the proposed core, loops, or interdomain junctions?", "kind": "measurement", "id": "domain-integrity-q01" }, { "text": "Does the evidence establish an intact fold, a disrupted state, or only an uncertain structural prediction?", "kind": "boundary", "id": "domain-integrity-q02" } ] } ] }, { "id": "permitted-inferences", "name": "Permitted inferences", "description": "Constrain annotation transfer and prioritize validation.", "findings": [ { "id": "evidence-bounded-use", "name": "Evidence-bounded use", "description": "Determine whether the occurrence supports membership annotation, subtype assignment, interface comparison, or a functional hypothesis.", "questions": [ { "text": "Which claims can be transferred from classified relatives, and which require direct evidence for this domain?", "kind": "action", "id": "evidence-bounded-use-q01" }, { "text": "Would boundary refinement, structural validation, or a domain-specific interaction assay resolve the most consequential uncertainty?", "kind": "action", "id": "evidence-bounded-use-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The registry label needs an authoritative database mapping to settle whether it denotes a particular homologous superfamily or a broader structural grouping.", "The listed domain types are conventional immunoglobulin-domain categories, not an exhaustive classification of all immunoglobulin-like folds.", "This is recalled knowledge without source verification; the entry describes a protein-domain class rather than a single chemical substance with fixed physical constants." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Variable-type (V-set) domains", "Constant-1-type (C1-set) domains", "Constant-2-type (C2-set) domains", "Intermediate-type (I-set) domains" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "InterPro accession", "value_or_pattern": "IPR followed by six digits", "note": "InterPro distinguishes domain families and homologous superfamilies; the exact record intended by this registry label requires verification." }, { "scheme": "Pfam accession", "value_or_pattern": "PF followed by five digits", "note": "Individual immunoglobulin-like domain families have separate accessions; one family record does not necessarily cover the entire superfamily." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Antigen recognition by antibody and T-cell receptor domains.", "Cell adhesion and recognition through immunoglobulin-superfamily cell-surface proteins.", "Protein engineering of antibody fragments and other binding scaffolds.", "Structural and evolutionary annotation of protein sequences." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Domain length", "typical_range": "Approximately 70-130 for many conventional immunoglobulin-like domains; insertions and boundary definitions produce exceptions", "unit": "amino acid residues" }, { "quantity": "Beta-strand count", "typical_range": "Commonly 7-9 in conventional immunoglobulin domains; varies by subtype", "unit": "beta strands per domain" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Mutations can disrupt domain folding, stability, binding or cell-surface expression.", "Some immunoglobulin domains can misfold and aggregate; antibody light-chain domains can participate in amyloid deposition.", "Sequence divergence can cause domain-detection methods to miss genuine members or assign uncertain boundaries.", "Similar folds alone do not establish equivalent function or a specific evolutionary relationship." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Immunoglobulin", "difference": "An immunoglobulin is an antibody protein assembled from multiple domains; an immunoglobulin-like domain is a structural module also found in non-antibody proteins." }, { "name": "Immunoglobulin superfamily", "difference": "This commonly groups whole proteins containing related immunoglobulin domains, whereas the requested label describes domains; database usage can overlap." }, { "name": "Immunoglobulin-like fold", "difference": "A fold describes structural topology; assignment to a homologous superfamily additionally implies evolutionary relatedness." }, { "name": "Fibronectin type III domain", "difference": "It has a related beta-sandwich architecture but is distinguished by sequence and structural classification; its inclusion in broader immunoglobulin-like groupings depends on the classification system." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does registry provenance establish exact equivalence to InterPro IPR036179, or does the name denote a broader grouping?", "Which domain families lie within the intended superfamily boundary, particularly where structural classifications disagree?", "Which subtype vocabulary covers the intended membership without forcing atypical domains into antibody-derived categories?", "What evidence thresholds should govern acceptance of remote, partial, or structure-only domain assignments?", "Should PHY / PHY.MAT be retained for this classification of molecular domains, or reviewed separately as a registry placement issue?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }